test

cmt/camel_setup.sh

@@ -79,3 +79,4 @@ echo "your CAMELROOT is $CAMELROOT"
 
 # put 1 at the end of next line if you want a closer look at compilaton
 export VERBOSE=
+echo "if you want more verbose compilation define VERBOSE environement variable to 1: export VERBOSE=1"

cmt/requirements-gcc

@@ -3,12 +3,13 @@ package CAMEL
 use class HEAD
 
 #compiler options
-#macro cpp "icpc"
-#macro cppflags " -O2  -ip -ansi_alias -align -Wbrief "
-
 #default is gcc here are the C++ compiler options
-macro cppflags " -O2 -pipe -ansi -Woverloaded-virtual -Wpedantic -Wunused -Wmaybe-uninitialized -Wno-deprecated -Wno-div-by-zero -Wno-variadic-macros"
-macro cflags  " -O2  -fopenmp "
+macro cppflags " -O3  -pipe -ansi -Woverloaded-virtual -Wpedantic -Wunused -Wmaybe-uninitialized -Wno-deprecated -Wno-div-by-zero "
+
+# although it may be strange we do not compile CAMEL with OMP because CLASS is not thread safe
+# no worries: CLASS is compiled with OMP
+#macro_append cppflags "-fopenmp "
+macro_append cpplinkflags  " -fopenmp "
 
 
 #CAMEL includes
@@ -23,8 +24,9 @@ include_dirs  "../src/camel/JLA/jla_likelihood_v3/src"
 
 
 #cfitsio
-include_dirs "$(CLIKDIR)/include"
-macro_append  CAMEL_linkopts " -L$(CLIKDIR) -lcfitsio"
+#include_dirs "$(CLIKDIR)/include"
+#macro_append  CAMEL_linkopts " -L$(CLIKDIR) -lcfitsio"
+macro_append  CAMEL_linkopts " -lcfitsio"
 
 #JLA :requires cblas/lapack
 macro_append cppflags ' -DJLA '
@@ -34,9 +36,9 @@ application test_jla -group=test -s=../src/camel test/test_jla.cc
 
 
 #PLANCK
-macro_append cppflags " -DCLIK  $(CLIKCFLAGS)"
-macro_append cflags " -DCLIK  $(CLIKCFLAGS)"
-macro_append  CAMEL_linkopts " $(CLIKLIBS) "
+#macro_append cppflags " -DCLIK  $(CLIKCFLAGS)"
+#macro_append cflags " -DCLIK  $(CLIKCFLAGS)"
+#macro_append  CAMEL_linkopts " $(CLIKLIBS) "
 
 #include_dirs "$(CLIKDIR)/include"
 #include_dirs  "$(CLIKDIR)/src"
@@ -47,13 +49,13 @@ macro_append  CAMEL_linkopts " $(CLIKLIBS) "
 
 
 # PICO 
-macro_append cppflags " -DPICO $(PICOINC) "
-macro_append CAMEL_linkopts " -L$(PICO_CODE) -lpico -lpython2.7 "
+#macro_append cppflags " -DPICO $(PICOINC) "
+#macro_append CAMEL_linkopts " -L$(PICO_CODE) -lpico -lpython2.7 "
 # the previous line should be sufficient otherwise try the PICOLIBS 
 # (set in camel_setup.sh)
 #macro_append CAMEL_linkopts " $(PICOLIBS)"
-macro_append cppflags ' -DPICODATA=\"$(PICO_DATA)\" '
-application testPico -group=test -s=../src/camel/pico/exec testPico.cc
+#macro_append cppflags ' -DPICODATA=\"$(PICO_DATA)\" '
+#application testPico -group=test -s=../src/camel/pico/exec testPico.cc
 
 ###FROM THERE YOU DONT NEED TO TOUCH
 ###########################################################################################

lik/BAO/BAO1D_dr12_mgs.lik

+# for adding comment # followed by a space (only on a new line)
+# input data for BAO
+# in/fix | name | num of data | z | value | error | out of diag| elements (eventually)
+in 6dF 1 0.106 457 27
+fix SDSS(R) 1  0.35 8.88 0.17
+fix BOSS(DR9) 1 0.57 13.67 0.22
+fix BOSS-CMASS(DR11) 1 0.57 2056 20 
+fix BOSS-LOWZ(DR11) 1 0.32 1264 25 
+fix WiggleZ 3 0.44 0.0916 0.0071 0.60 0.0726 0.0034 0.73 0.0592 0.0032 0.003068 0.0 0.00222005 
+fix SDSS 2 0.20 0.1905 0.0061 0.35 0.1097 0.0036 0.002723
+in  SDSS-MGS   1 0.15 664 25 

lik/BAO/BAO1D_new_mgs.lik

+# for adding comment # followed by a space (only on a new line)
+# input data for BAO
+# in/fix | name | num of data | z | value | error | out of diag| elements (eventually)
+in 6dF 1 0.106 457 27
+fix SDSS(R) 1  0.35 8.88 0.17
+fix BOSS(DR9) 1 0.57 13.67 0.22
+fix BOSS-CMASS(DR11) 1 0.57 2056 20 
+in BOSS-LOWZ(DR11) 1 0.32 1264 25 
+fix WiggleZ 3 0.44 0.0916 0.0071 0.60 0.0726 0.0034 0.73 0.0592 0.0032 0.003068 0.0 0.00222005 
+fix SDSS 2 0.20 0.1905 0.0061 0.35 0.1097 0.0036 0.002723
+in  SDSS-MGS   1 0.15 664 25 

par/examples/hlpPS_tauprior.par

+###############################################################
+#Boltzman Engine
+engine=pico
+
+
+
+###############################################################
+#Cosmological model
+par   omega_b             cosm    0.02224     0.00027   0.017   0.027
+par   omega_cdm           cosm    0.1192      0.0026    0.09    0.15
+par   100*theta_s         cosm    1.0418      0.6E-04   1.03	1.05
+par   tau_reio            cosm    0.07	      0.13E-01  0.01	0.20
+par   log(10^10A_s)       cosm    3.07	      0.025     2.7     3.5
+par   n_s                 cosm    0.96	      0.0070    0.9     1.1
+###############################################################
+
+
+gauss1    tau_reio	0.058	0.012
+
+
+###############################################################
+#LIKELIHOODS
+
+
+#-----------------------------
+#CMB high-l (HILLIPOP)
+Hillipop=HiLLiPOP/DX11dHM_superExt_CO_TT.lik
+par   A_planck     	  nui	  1.		0.001	     0.9 	1.1
+par   c0		  nui     0.		0.001     -0.05   0.05
+par   c1		  nui     0.		0.001     -0.05   0.05
+fix   c2		  nui     0.		0.001     -0.05   0.05
+par   c3		  nui     0.		0.001     -0.05   0.05
+par   c4		  nui     0.004		0.001     -0.05   0.05
+par   c5		  nui     0.004		0.001     -0.05   0.05
+par   Aradio		  nui     1.		1E-01     0.0     2
+par   Adusty		  nui     1.		1E-01     0.0     2
+par   Asz                 nui     1.		0.1       0.0     10
+par   Acib                nui     1.		0.1       0.0     10
+par   AdustTT		  nui	  1.	        0.1	  0.0     2
+fix   AdustPP		  nui	  0.		0.1	  0.0     2
+fix   AdustTP		  nui	  0.		0.1	  0.0     2
+par   Aksz                nui     0.		1.0	  0.0     10
+par   Aszxcib             nui     0.		1.0	  0.0     10
+
+#PRIORS
+gauss1    AdustTT	1	0.2
+gauss1    Asz		1	0.2
+gauss1    Acib		1	0.2
+gauss1    Aradio	1	0.2
+gauss1    Adusty	1	0.2
+gauss1    A_planck	1	0.0025
+gauss1    c0		0	2e-3
+gauss1	  c1		0	2e-3
+gauss1	  c3		0	2e-3 
+gauss1	  c4		0.002	2e-3 
+gauss1	  c5		0.002	2e-3 
+#-----------------------------
+
+
+###############################################################
+
+
+
+
+###############################################################
+#pico neutrino setup
+# 1 degenerated massive neutrino
+fix          m_ncdm          cosm       0.06 
+fix          N_nu            cosm       3.046
+fix          YHe             cosm       0.248
+fix          Alens           cosm       1
+###############################################################
+
+
+###############################################################
+#fitter
+nitermax=50000
+set_stra=2
+set_tol=0.00001
+
+#output options
+remove_cosmo_limits=false
+doHesse=true
+###############################################################

src/camel/BAO/BAO_chi2.cc

@@ -64,6 +64,8 @@ double BAO_chi2::chi2_eff(const std::vector<double>& par) const
     if((_data_name[i]=="BOSS-CMASS(DR11)")&&(_data[i]==1421)) cosmo[i]=(engine->get_Da(_z[i]))*149.28/rs_drag;
     // if((_data_name[i]=="BOSS-CMASS(DR11)")&&(_data[i]==1421))  cout <<"Da(z=0.57) ="<< engine->get_Da(_z[i])  <<endl;
     if((_data_name[i]=="BOSS-CMASS(DR11)")&&(_data[i]==96.8)) cosmo[i]=(engine->get_H(_z[i]))*rs_drag/149.28;
+    if((_data_name[i]=="SDSS-MGS")&&(_data[i]==664.)) cosmo[i]=engine->get_Dv(_z[i])*rs_drag/149.69;
+    //cout << " _data_name[i] "<< cosmo[i]<<" "<< _data[i] << endl;
     // if((_data_name[i]=="BOSS-CMASS(DR11)")&&(_data[i]==96.8))  cout <<"H(z=0.57) ="<< engine->get_H(_z[i])  <<endl;
   }
 
@@ -75,7 +77,7 @@ double BAO_chi2::chi2_eff(const std::vector<double>& par) const
   //chi2 actual calculation
   HepVector diff;
   diff=cosmo-_data;
-
+  
   //this computes xT*_inv_cov*x
   chi2=_inv_cov.similarity(diff); 
   //cout<< "chi2 bao="<< chi2 <<endl;

src/camel/Chi2Combiner.cc

@@ -86,15 +86,10 @@ Chi2Combiner::chi2_eff(const std::vector<double>& par) const {
       copy(par.begin(),par.end(),ostream_iterator<double>(os,"\t"));
     }
 
-    //update Engine
-
-    //1 seul thread
-    
-#pragma omp critical 
+#pragma omp critical
     {
       self->OK=engine->updateParValues(par);
     }
-
     if (!OK) {
       //A TUNER!!!!!!!!!!!!!1
       chi2=chi2_prev*10.;

src/camel/Class/ClassEngine.cc

@@ -623,7 +623,7 @@ double ClassEngine::get_Dv(double z)
   double *pvecback;
   //transform redshift in conformal time
   background_tau_of_z(&ba,z,&tau);
-  cout << " dv : tau= "<< tau <<endl;
+//   cout << " dv : tau= "<< tau <<endl;
   //pvecback must be allocated 
   pvecback=(double *)malloc(ba.bg_size*sizeof(double));
 

src/camel/exec/writeSpectraPk.cc

@@ -15,18 +15,17 @@ using namespace std;
 
 
 
-vector<double> logspace(double kmin,double kmax, int npks){
+void logspace(double kmin,double kmax, int npks,vector<double>&v){
 
   double lmax=std::log(kmax);
   double lmin=std::log(kmin);
   double step=(lmax-lmin)/(npks-1);
 
-  vector<double> v(npks);
+  v.resize(npks);
   for (size_t i=0;i<npks;i++){
     double lval=lmin+step*i;
     v[i]=std::exp(lval);
   }
-  return v;
 
 }
 
@@ -59,11 +58,11 @@ int main(int argc,char** argv){
     classparms.add("z_pk",z0); //polar +lens+clphi
     classparms.add("z_max_pk",z0); //polar +lens+clphi
 
-    int do_nl =0;
+    bool do_nl =false;
     try{
       size_t test =  classparms.findIndex("non linear");
       cout << " >>> CLASS nl par found !! "<< test<<endl;
-      do_nl = 1 ;
+      do_nl = true;
     }catch (Message_error& msg){
       
       cout << " >>> CLASS nl par NOT found !! " <<endl;      
@@ -89,28 +88,33 @@ int main(int argc,char** argv){
     double H0=e->get_H0();
     double h=H0/100;
     double theta=e->theta();
-    cout << " expansion: H0=" << H0 << " 100*theta_s=" << 100*theta << endl << endl;;
+    cout << endl << " expansion: H0=" << H0 << " 100*theta_s=" << 100*theta << endl;
     cout << " Omega_m=" << e->Omega_m() << " Omega_m*h2=" << e->Omega_m()*h*h << endl ;
 
     //reio
     double tau=e->get("tau_reio");
     double zreio=e->get("z_reio");
-    cout << " reio : tau_reio=" << tau << " z_reio=" << zreio << endl << endl;;
-
-    //sigma8
-    double s8=e->get_sigma8(0.);
-    cout << " sigma8=" << s8 << endl;
-    cout << " f sigma8=" << e->get_f(0.)*e->get_sigma8(0.) << endl;
-    
+    cout << " reio : tau_reio=" << tau << " z_reio=" << zreio << endl ;
 
     //YHE
-    cout << " YHe=" << e->YHe() << endl << endl;;
+    cout << " YHe=" << e->YHe() << endl;
 
-     cout << "recombination: zrec=" << e->z_rec() << " rs(zrec)=" << e->rs_rec() << endl;
+     cout << " recombination: zrec=" << e->z_rec() << " rs(zrec)=" << e->rs_rec() << endl;
     //BAO
 
-    cout << "BAO: zd=" << e->z_drag() << " rs(zd)=" << e->rs_drag() << endl;
+    cout << " BAO: zdrag=" << e->z_drag() << " rs(zd)=" << e->rs_drag() << endl;
+
+    //sigma8/f
+    cout <<" z0="<< z0 << "-> sigma8=" << e->get_sigma8(z0) << " f=" << e->get_f(z0)<< " f*sigma8=" << e->get_sigma8(z0)*e->get_f(z0) <<endl << endl;
 
+    /*
+    double zval[]={0.,0.5,1.,1.5,2.};
+    const int nval=sizeof(zval)/sizeof(double);
+    for (size_t i=0;i<nval;i++){
+      double z=zval[i];
+      //cout << "z=" << z<< ": s8=" << e->get_sigma8(z) << ", f=" << e->get_f(z)<< ", f*s8=" <<  e->get_sigma8(z)*e->get_f(z)<< endl;
+    }
+    */
 
     //ecriture output fits
   const std::string fileName(argv[3]);
@@ -180,10 +184,10 @@ int main(int argc,char** argv){
     }
   }
 
-  // pk 
 
+  // pk 
   cout << "Computing P(k) at z=" << z0 << endl;
-  cout << "NL spectrum will" << (do_nl==0? " NOT ":" ") << "be computed" <<endl;
+  cout << "NL spectrum will" << (!do_nl? " NOT ":" ") << "be computed" <<endl;
 
   //ecriture output fits
   std::vector<fitscolumn> pkcols;
@@ -192,27 +196,39 @@ int main(int argc,char** argv){
   pkcols.push_back(fitscolumn("Pknl", "(1/Mpc)^-3",1,TDOUBLE));
   fout.insert_bintab(pkcols);
 
+  // def values
+  vector<double>  kval;
+
+  string kvfile=parser.params.find<string>("kval_file","");
+  if (kvfile.size()!=0) {
+    ifstream f(kvfile.c_str());
+    double kk;
+    while (f>>kk) kval.push_back(kk);
+  }
+  else{
+  const int npks = parser.params.find<int>("n_pks",1000);
+  const double kmin = parser.params.find<double>("k_beg",8.e-4);
+  const double kmax = parser.params.find<double>("k_end",1);
+  logspace(kmin,kmax,npks,kval) ; 
+
+  }
 
-  const int npks = 1000 ;
-  const double kmin = 8.e-4;
-  const double kmax = 5;
-  vector<double>  kval=logspace(kmin,kmax,npks) ; 
 
   vector<double>  pklin;
   vector<double>  pknl ;
-  for (int k =0; k<npks ; k++){
+  for (int k =0; k<kval.size() ; k++){
     double myk=kval[k];
     pklin.push_back( e->get_Pk(myk,  z0)   );
-    if ( do_nl == 1) pknl.push_back(  e->get_PkNL(myk,  z0) );
+    if ( do_nl ) pknl.push_back(  e->get_PkNL(myk,  z0) );
 
   }
-  arr<double> apk(npks);
-  for (size_t i=0; i<npks ; i++) apk[i]=kval[i];
+  arr<double> apk(kval.size());
+  for (size_t i=0; i<kval.size() ; i++) apk[i]=kval[i];
   fout.write_column(1,apk);
-  for (size_t i=0; i<npks ; i++) apk[i]=pklin[i];
+  for (size_t i=0; i<kval.size() ; i++) apk[i]=pklin[i];
   fout.write_column(2,apk);
-  if ( do_nl == 1){
-    for (size_t i=0; i<npks ; i++) apk[i]=pknl[i];
+  if ( do_nl ){
+    for (size_t i=0; i<kval.size() ; i++) apk[i]=pknl[i];
     fout.write_column(3,apk);
   }
 

work/batch/cc/Profile.sh

@@ -138,14 +138,14 @@ echo "fix  $var  \$type  $zeval" >>   parfile_in
 
 #special case of degenerate neutrinos (need to decrement Neff by 1 when mass=0)
 if [ "$var" == "m_ncdm" ] ; then
-grep -v ncdm parfile_in | grep -v N_eff > tmp
+grep -v ncdm parfile_in | grep -v N_ur > tmp
 
 if [ "$zeval" == "0" ] ; then
-echo "class N_eff   3.046" >> tmp
+echo "class N_ur   3.046" >> tmp
 echo "fix N_ncdm  cosmo 0" >> tmp
 else
 echo "class  N_ncdm    1" >>  tmp
-echo "class N_eff   2.046" >> tmp
+echo "class     N_ur                 2.0328" >> tmp
 echo "fix  m_ncdm  cosmo $zeval" >> tmp
 fi
 

work/tools/idl/mnufit.pro

@@ -69,7 +69,7 @@ endfor
 cgplot,[0,0],yr,/over
 
 
-al_legend,label,textcol=cgcolor(cols),box=0,pos=[0.05,0.85],/norm
+;al_legend,label,textcol=cgcolor(cols),box=0,pos=[0.05,0.85],/norm
 
 if keyword_set(write) then closeplot,_extra=extra_keywords